Tutorial 01 - shuaigroup · 2020. 1. 16. · MOMAP Tutorial - Fluorescence Spectrum Calculation...

MOMAP

Tutorial 01 Fluorescence Spectrum Calculation

Version 2019 September, 2019

MOMAP Tutorial 01

Version 2019 edited by:

Dr. Qikai Li

Dr. Yingli Niu

Ms. Lihui Yan

Released by Hongzhiwei Technology (Shanghai) Co., Ltd

and Z.G. Shuai Group

The information in this document applies to version 2019 of MOMAP

MOMAP Tutorial - Fluorescence Spectrum Calculation

Azulene is an organic compound and an isomer of naphthalene. Whereas naphthalene is colorless,

azulene is dark blue. Two terpenoids, vetivazulene (4,8-dimethyl-2-isopropylazulene) and guaiazulene (1,4-

dimethyl-7-isopropylazulene), that feature the azulene skeleton are found in nature as constituents of

pigments in mushrooms, guaiac wood oil, and some marine invertebrates.

MOMAP is able to simulate fluorescence spectrum and calculate the corresponding radiative decay rate

constant based on the TVCORF_SPEC and TVSPEC_SPEC subprograms. The TVCORF_SPEC subprogram is

used to calculate thermal vibration correlation function (TVCF), while the TVSPEC_SPEC subprogram is used

to simulate fluorescence spectrum.

To begin the TVCORF_SPEC and TVSPEC_SPEC calculations, we need the evc results. The evc calculation

can use outputs from other QC programs, such as Gaussian, TURBOMOLE, ChemShell, Dalton, MOLPRO, DFTB

and MOPAC etc. It can also read data from the output files, including vibrational frequencies and force

constant matrix, and calculate normal mode displacement, Huang-Rhys factor, reorganization energy and

Duschinsky rotation matrix between initial and final electronic states under both internal coordinate and

Cartesian coordinate.

Thus, the basic steps involved in the calculations are as follows:

1. Gaussian calculations

2. Vibration analysis etc.

3. Fluorescence spectrum calculation

Contents

Gaussian Calculations ....................................................................................................................................................................... 1 Optimization calculation on ground state (S0) ................................................................................................................ 1 Optimization calculation on lowest singlet excited state (S1) ..................................................................................... 2 Calculate non-adiabatic coupling matrix element (NACME) ..................................................................................... 3

Vibration Analysis ............................................................................................................................................................................... 5 Adiabatic Excitation Energy ............................................................................................................................................................ 7 Electronic Transition Dipole ............................................................................................................................................................ 8 Fluorescence Spectrum Calculation ........................................................................................................................................... 10

Nonradiative rate kic ............................................................................................................................................................... 10 Radiative rate kr ........................................................................................................................................................................ 13

Sum-over-states Approach .......................................................................................................................................................... 17 Verify Convergence of Correlation Function .......................................................................................................................... 20

1

Gaussian Calculations

Optimization calculation on ground state (S0)

Once the initial geometry is obtained, we have to find the optimized S0 geometry. The route section is set as

#p opt b3lyp/6-31g*, which indicates an optimization calculation at B3LYP/6-31G* level.

The initial geometry gaussian S0 input file (azulene-s0.com) is as follows:

We use g09 or g16 to do the geometry optimization.

Fig. 1 Optimized S0 geometry

%chk=azulene-s0.chk

%mem=4GB

%nprocl=1

%nprocs=8

#p opt freq B3LYP/6-31G*

azulene-s0 optimization

0 1

C 2.01378743 -1.48849852 0.00000000

C 2.28995141 -0.11795315 0.00000000

C 1.39185815 0.95357383 0.00000000

C 0.78413689 -2.15418449 0.00000000

C 0.00000000 0.93285810 0.00000000

C -0.50398383 -1.61065958 0.00000000

C -0.89316505 -0.27406276 0.00000000

H 2.88919252 -2.13621797 0.00000000

H 3.34387207 0.15083266 0.00000000

H 1.84191311 1.94635990 0.00000000

H 0.83658347 -3.24058384 0.00000000

H -1.32037398 -2.33298523 0.00000000

C -0.84567310 2.05536637 0.00000000

H -0.51364908 3.08694089 0.00000000

C -2.17758707 1.61062710 0.00000000

H -3.04994479 2.25593917 0.00000000

C -2.21339978 0.20656494 0.00000000

H -3.10314368 -0.41207657 0.00000000

2

Optimization calculation on lowest singlet excited state (S1)

With the optimized S0 geometry at hand, we can start optimizing S1 geometry using the optimized S0

geometry as the initial structure. The route section is set as #p td opt b3lyp/6-31g*, which indicates

an optimization calculation at B3LYP/6-31G* level using the TDDFT method.

The initial gaussian S1 input file (azulene-s1.com) is as follows:

Again, use g09 or g16 to do the S1 optimization.

Fig. 2 Optimized S1 geometry

%chk=azulene-s1.chk

%mem=4GB

%nprocl=1

%nprocs=8

#p opt freq td B3LYP/6-31G*

azulene-s1 optimization

0 1

C 2.01378700 -1.48849900 0.00000000

C 2.28995100 -0.11795300 0.00000000

C 1.39185800 0.95357400 0.00000000

C 0.78413700 -2.15418400 0.00000000

C 0.00000000 0.93285800 0.00000000

C -0.50398400 -1.61066000 0.00000000

C -0.89316500 -0.27406300 0.00000000

H 2.88919300 -2.13621800 0.00000000

H 3.34387200 0.15083300 0.00000000

H 1.84191300 1.94636000 0.00000000

H 0.83658300 -3.24058400 0.00000000

H -1.32037400 -2.33298500 0.00000000

C -0.84567300 2.05536600 0.00000000

H -0.51364900 3.08694100 0.00000000

C -2.17758700 1.61062700 0.00000000

H -3.04994500 2.25593900 0.00000000

C -2.21340000 0.20656500 0.00000000

H -3.10314400 -0.41207700 0.00000000

3

Calculate non-adiabatic coupling matrix element (NACME)

Unlike rad_FL calculation, The NACME should be obtained before performing a nonrad

calculation.

After finding the optimized S1 geometry, we can calculate NACME at this geometry.

The route section is set as the following line:

#p td b3lyp/6-31g(d) prop=(fitcharge,field) iop(6/22=-4, 6/29=1, 6/30=0, 6/17=2)

The initial gaussian nacme input file (azulene-nacme.com) is as follows:

Again, use g09 or g16 to do the NACME calculation.

Now, all the Gaussian related calculations are done.

In the following calculations, we need the gaussian *.fchk files, we use the Gaussian built-in command

formchk to generate the *.fchk file based on output *.chk. The *.fchk file contains readable force constant

matrix information that is needed in dushin calculation.

TIPS: To obtain the optimized ground state geometry, use Gaussview to open azulen-s0.log file,

and save as azulene-s1.com. Then, modify the first few lines of azulene-s1.com to suit for S1

optimization.

%chk=azulene-nacme.chk

%mem=4GB

%nprocl=1

%nprocs=8

#p td B3LYP/6-31G* prop=(fitcharge,field) iop(6/22=-4,6/29=1,6/30=0,6/17=2) nosymm

azulene excited state nacme calculation

0 1

C 2.00781300 -1.54567700 0.00000000

C 2.29335100 -0.16097300 0.00000000

C 1.43666200 0.92263700 0.00000000

C 0.74217000 -2.17592100 0.00000000

C 0.00000000 0.87899800 0.00000000

C -0.52457900 -1.62505800 0.00000000

C -0.85006100 -0.22497100 0.00000000

H 2.86853900 -2.20838800 0.00000000

H 3.35493800 0.08558900 0.00000000

H 1.88767400 1.91181300 0.00000000

H 0.77544500 -3.26524800 0.00000000

H -1.36541000 -2.31420500 0.00000000

C -0.84651000 2.06953900 0.00000000

H -0.46545900 3.08512900 0.00000000

C -2.19214700 1.68790200 0.00000000

H -3.04949000 2.34818800 0.00000000

C -2.21739500 0.28941600 0.00000000

H -3.10206800 -0.33823600 0.00000000

4

$ formchk azulene-s0.chk

$ formchk azulene-s1.chk

$ formchk azulene-nacme.chk

TIPS: To obtain the optimized excited state geometry for NACME calculation, use Gaussview to open

azulen-s1.log file, and save as azulene-nacme.com. Then, modify the first few lines of azulene-

nacme.com to suit for NACME calculation.

5

Vibration Analysis

The evc calculation requires the basic information on initial and final electronic states. Thus, to begin

an evc calculation, you need to designate the related file names in MOMAP input file (i.e., momap.inp).

For the Gaussian output files, you have to provide the corresponding .fchk files as well, as done in the

last section.

The momap.inp for evc calculation is straightforward and is shown as follows:

Copy the following gaussian output files from upper directory:

../gaussian/azulene-s0.fchk

../gaussian/azulene-s0.log



to this evc work directory.

A run file is also created, and is shown as follows:

[evc]$ cat momap.inp

do_evc = 1 # toggle dushin rotation effect, 1 or 0

&evc

ffreq(1) = "azulene-s0.log" # log file of ground state

ffreq(2) = "azulene-s1.log" # log file of excited state /

TIPS: In each directory, there exists a README file, just follow the instructions in README to carry

out the operations. For example, the README in evc is shown as follows:

How to run MOMAP

1) Copy the following gaussian files from upper directory:



../gaussian/azulene-t1.fchk

../gaussian/azulene-t1.log

to this directory.

2) Change momap.inp accordingly.

3) Run MOMAP to do the calculation by the following command:

./run

#!/bin/sh

momap -input momap.inp -np 4

6

Users may modify the run file, for example, by changing the np option from 4 to 8, and perform the

calculation by running the script file:

$ ./run

The result files are as follows:

evc.cart.dat: includes frequency, Huang−Rhys factor, and Duschinsky matrix (Cartesian coordinate

system).

evc.dint.dat: includes frequency, Huang−Rhys factor, and Duschinsky matrix (D solved by using internal

coordinate system).

evc.cart.abs: Duschinsky matrix file, used to plot 2D Duschinsky figure.

evc.cart.nac: Projection of NACME to normal modes.

evc.cart.inp: Projection of derivatives of transition dipoles to normal modes.

evc.dx.x.com: Molecular overlapping figure of two electron states (viewed by using Gaussview)

evc.dx.x.xyz: Molecular overlapping figure of two electron states (viewed by using Jmol)

evc.dx.v.xyz: Molecular displacement vectors of two electron states (viewed by using Jmol)

evc.vib1.xyz: Molecular vibrational vectors at ground state (viewed by using Jmol)

evc.vib2.xyz: Molecular vibrational vectors at excited state (viewd by using Jmol)

evc.out: evc log file

Except for ffreq(1) and ffreq(2) parameters, the evc program also allows user to project

reorganization energy onto the internal coordinate, to take account of isotope effect, and to configure many

other advanced settings etc., please refer to the MOMAP User Guide for details.

Please check the reorganization energy results between evc.cart.dat and evc.dint.dat. If the

energy difference is small (< 1000 cm-1), then use the results in evc.cart.dat to do the next calculations.

However, if the energy difference is large, then use evc.dint.dat to do the next calculations.

evc.dx.x.com evc.dx.v.xyz

Electron vibration coupling

[evc]$ ls

azulene-nacme.log azulene-s1.log evc.dint.dat evc.out nodefile

azulene-s0.fchk evc.cart.abs evc.dx.v.xyz evc.vib1.xyz README

azulene-s0.log evc.cart.dat evc.dx.x.com evc.vib2.xyz ref

azulene-s1.fchk evc.dint.abs evc.dx.x.xyz momap.inp run

7

Adiabatic Excitation Energy

Before we can calculate the Fluorescence Spectrum, we need to known the adiabatic excitation energy

Ead. The adiabatic excitation energy is the energy difference between the relaxed excited state energy and the

ground state energy.

From the S0 Gaussian log file, locate the last line with “SCF Done” in the output azulene-s0.log file

in order to find the single point energy at the optimized S0 geometry.

For example, you may use the following commands:

$ cat azulene-s0.log | grep “SCF Done”

In this example, the last line with “SCF Done” is like the following:

SCF Done: E(RB3LYP) = - 385.838172128 A.U.

Thus, we have the energy Egs at optimized ground state geometry:

Egs = - 385.838172128 a.u.

From the S1 Gaussian log file, locate the last line with “Total Energy, E(TD-HF/TD-KS)” in the

output azulene-s1.log file in order to find the single point energy at the optimized S1 geometry.

For example, you may use the following commands:

$ cat azulene-s1.log | grep “Total Energy, E(TD-HF/TD-KS)”

In this example, the last line with “Total Energy, E(TD-HF/TD-KS)” is like the following:

Total Energy, E(TD-HF/TD-KS) = -385.763080213

Then, we have the single point energy Ees at the optimized S1 geometry:

Ees = - 385.763080213 a.u.

From the above obtained ground state S0 and excited state S1 energies, we can obtain the adiabatic

excitation energy Ead:

Ead = Ees - Egs = [(-385.763080213) - (-385.838172128)] a.u

= 0.075092 a.u

TIPS: To find the energies, users may use Gaussview to open the Gaussian log file, from the menu item

Results Summary to obtain the value, which is valid for both the ground state and excited state.

8

Electronic Transition Dipole

To calculate the spectrum by using the sum-over-states approach, we need the electronic

transition dipole data.

The Gaussian log file for the optimized S1 excited state has already included the Dipole Square

of Electronic Transition Dipole Absorption (EDMA) and the Dipole Square of Electronic Transition

Dipole Emission (EDME) information.

Open azulene-s1.log file with vim, for example, search the string “transition electric

dipole moments”, the first match is shown as follows:

Focus on the “Dip. S.” column, this is the Dipole Square of the calculated Electronic Transition

Dipole Absorption (EDMA), take note the data of the first excited state, i.e., 0.1330, this is the value

of the expected EDMA. Thus, we have:

trans =2

trans = 0.1330 a.u. = 0.36469 a.u.

= 0.36469 a.u.×2.5417 Debye/a.u.

= 0.92694 Debye

This is the value of parameter EDMA needed in our momap.inp file.

If the Linux command vim is used, press SHIFT + N, the search jumps to the last occurrence

of “transition electric dipole moments”, shown as follows:

9

Again, focus on the “Dip. S.” column, this is the Dipole Square of the calculated Electronic

Transition Dipole Emission (EDME), take note the data of the first excited state, i.e., 0.0649, this is

the value of the expected EDME. Thus, we have:

trans =2

trans = 0.0649 a.u. = 0.254755 a.u.

= 0.254755 a.u.×2.5417 Debye/a.u.

= 0.64751 Debye

Again, this is the value of parameter EDME needed in our momap.inp file.

TIPS: If the optimization and frequency calculations are separate, then the data of EDME and EDMA should

be taken from the log file of excited state geometry optimization.

10

Fluorescence Spectrum Calculation

Nonradiative rate kic

Create a directory kic and go to that directory, in this directory, we further create two directories evc

and kic.

To start the calculation, you need a *.dat file, a MOMAP control file, and optionally a parallel control

file. The *.dat file is obtained from the previous mentioned evc calculation. A MOMAP control file is used

to control how TVCORF_SPEC and TVSPEC_SPEC subprograms behavior. An optional parallel control file

is used to control how many computing processes will be used.

To begin with, the first step is to do an evc calculation. Note we also need the non-adiabatic coupling

matrix element (NACME) calculation log file, that is, azulene-nacme.log, to do the nonradiative rate

calculation.

Go to the directory evc, copy the following gaussian files from upper directory:

../../gaussian/azulene-s0.fchk

../../gaussian/azulene-s0.log

../../gaussian/azulene-s1.fchk

../../gaussian/azulene-s1.log

../../gaussian/azulene-nacme.log

to this work directory.

Create a momap.inp file with its contents as follows:

Also create a run file and change it with execution attribute (e.g., chmod a+rx run), the run file is

very simple, and is shown as follows:



$ ./run

When the calculation finishes, the result files are as follows:

[kic/evc] cat momap.inp

do_evc = 1

&evc

ffreq(1) = "azulene-s0.log" # log file of ground state

ffreq(2) = "azulene-s1.log" # log file of excited state

fnacme = "azulene-nacme.log" # log file of NACME /

#!/bin/sh

momap -input momap.inp -np 4

11

Please check the reorganization energy results between evc.cart.dat and evc.dint.dat. If the

energy difference is small (< 1000 cm-1), then use the results in evc.cart.dat to do the next calculations.

However, if the energy difference is large, then use evc.dint.dat to do the next calculations.

For example, we can use the Linux command cat and grep to do the job:

$ cat evc.cart.dat evc.dint.dat | grep "Total reorganization energy"

Total reorganization energy (cm-1): 3390.305348 3453.436666

Total reorganization energy (cm-1): 3412.711425 3449.528917

As can be seen, the energy difference is indeed rather small.

Once the evc calculation is done, we then go to the kic directory.

Copy the following evc files from upper directory:

../evc/evc.cart.dat

../evc/evc.cart.nac

to this kic work directory.

Create a momap.inp with its contents as follows:


shown as follows:

[kic/evc]$ ls

azulene-nacme.log azulene-s1.log evc.dint.abs evc.dx.x.xyz momap.inp run

azulene-s0.fchk evc.cart.abs evc.dint.dat evc.out nodefile

azulene-s0.log evc.cart.dat evc.dx.v.xyz evc.vib1.xyz README

azulene-s1.fchk evc.cart.nac evc.dx.x.com evc.vib2.xyz ref

[kic/kic]$ cat momap.inp

do_ic_tvcf_ft = 1 # toggle internal conversion correlation function, 1 or 0

do_ic_tvcf_spec = 1 # toggle internal conversion spectrum, 1 or 0

&ic_tvcf

DUSHIN = .t. # toggle Duschinsky rotation effect, .t. or .f.

Temp = 300 K # temperature

tmax = 1000 fs # integral interval of correlation function

dt = 1 fs # integration timestep of correlation function

Ead = 0.075092 au # adiabatic excitation energy difference between two states

DSFile = "evc.cart.dat" # input dushin file

CoulFile = "evc.cart.nac" # input nacme info file

Emax = 0.3 au # upper bound of spectrum frequency

logFile = "ic.tvcf.log" # output file for logging

FtFile = "ic.tvcf.ft.dat" # output file for correlation function info

FoFile = "ic.tvcf.fo.dat" # output file for spectrum function info /

#!/bin/sh

momap -input momap.inp -np 4 &> log &

12



$ ./run

When the calculation finishes, the result files are shown as follows:

The Internal conversion (IC) rate constant can be found at the end of ic.tvcf.log file. The relationship

between IC rate constant and energy gap can be obtained from ic.tvcf.fo.dat file.

Filename Meaning

ic.tvcf.fo.dat Output file for spectrum function

ic.tvcf.ft.dat Output file for correlation function

ic.tvcf.log Output file for logging

Then use the following commands to generate the correlation function plot to check for convergence:

$ gnuplot *.gnu

$ ps2png *.eps

$ display *.png

Fig. 3 Distribution of time vs real part of a converged correlation function

[kic/kic]$ ls

evc.cart.dat ic.tvcf.fo.dat ic.tvcf.log momap.inp README run

evc.cart.nac ic.tvcf.ft.dat ic.tvcf.ft.gnu log nodefile ref

13

Once the correlation function is known to be converged, we can obtain the nonradiative rate at the end

of the ic.tvcf.log file. From the file, we can obtain the internal conversion radiative rate kic for azulene

molecule is 1.92466768×1010 s-1，as shown below.

Radiative rate kr

Next, we create a directory kr and go to that directory.

Copy the following evc files from upper directory:

../evc/evc.cart.dat

to this kr work directory.



shown as follows:

[kr]$ cat momap.inp

do_spec_tvcf_ft = 1 # toggle correlation function calculation, 1 or 0

do_spec_tvcf_spec = 1 # toggle fluorescence spectrum calcluation, 1 or 0

&spec_tvcf

DUSHIN = .t. # toggle Duschinsky rotation effect, .t. or .f.

Temp = 300 K # temperature

tmax = 1000 fs # integration time

dt = 1 fs # integration timestep

Ead = 0.075092 au # adiabatic excitation energy

EDMA = 0.92694 debye # electronic dipole moment of absorption (GS)

EDME = 0.64751 debye # electronic dipole moment of emission (ES)

FreqScale = 1.0 # frequency scaling factor

DSFile = "evc.cart.dat" # input dushin file

Emax = 0.3 au # upper bound of spectrum frequency

dE = 0.00001 au # output energy interval

logFile = "spec.tvcf.log" # output file for logging

FtFile = "spec.tvcf.ft.dat" # output file for correlation function info

FoFile = "spec.tvcf.fo.dat" # output file for spectrum function info

FoSFile = "spec.tvcf.spec.dat" # output file for spectrum info /

14



$ ./run

When the calculation finishes, the result files are shown as follows:

The radiative decay rate constant can be found at the end of spec.tvcf.log file, while the

fluorescence spectrum information can be obtained from spec.tvcf.spec.dat.

Plot the data from file spec.tvcf.spec.dat by using columns 3, 5, and 6, in Linux, we can use

Gnuplot to do the plotting, the plot script is shown as follows:

Then use the following commands to generate the correlation and spectrum plots:

$ gnuplot *.gnu

$ ps2png *.eps

$ display *.png

#!/bin/sh


[kic/kic]$ ls

evc.cart.dat README spec.tvcf.ft.dat spec.tvcf.spec.gnu

log ref spec.tvcf.ft.gnu

momap.inp run spec.tvcf.log

nodefile spec.tvcf.fo.dat spec.tvcf.spec.dat

[sumstat]$ cat spec.tvcf.spec.gnu

reset

set nogrid

set lmargin 10

set pointsize 1.0

set encoding iso_8859_1

set term postscript eps enhanced color 20

set xlabel "Wave number, cm^{-1}" offset 0,0

set ylabel "Intensity, a.u." offset 0,0

set xtics nomirror

set ytics nomirror

set xrange [5000:30000]

set yrange [0:1.15]

set output "spec.tvcf.spec.eps"

plot \

"spec.tvcf.spec.dat" u 3:5 t "Absorption" w l lw 3 lt 1, \

"" u 3:6 t "Emission" w l lw 3 lt 2

15


Fig. 5 Absorption and emission spectrum

16

The script ps2png is used to convert a .eps file to .png file, with its contents as follows:

$ cat ~/bin/ps2png

#!/usr/bin/perl -w

#

# ps2png [resolution] file...

#

# Convert a postscript file to PNG, using the gs (GhostScript) command. The

# resolution defaults to 200, which is a readable compromise for most screens.

# The files should be postscript files. You can omit a .ps suffix and we'll

# assume it.

# Author: John Chambers

$ENV{LD_LIBRARY_PATH} = '/usr/X11R6/lib/:/usr/eecs/lib:/usr/lib:/usr/lib/aout';

if ( @ARGV == 0 )

{

print "Usage: ps2png [resolution] file...\n";

exit $?;

}

if (($res = $ARGV[0]) =~ /^\d+$/) {shift @ARGV} else {$res = 200}

file: for $file (@ARGV) {

if ($file =~ /(.*)\.(\w*ps)$/i) {

$fili = $file;

$filo = "$1.png";

} else {

if (-f ($fili = "$file.ps" )) {$filo = "$file.png";

} elsif (-f ($fili = "$file.eps")) {$filo = "$file.png";

} elsif (-f ($fili = "$file.PS" )) {$filo = "$file.PNG";

} else {

print STDERR "Can't find postscript file for $file.\n";

next file;

}

}

system "gs -q -DNOPAUSE -sDEVICE=ppmraw -r$res -sOutputFile='|pnmcrop|pnmtopng > $filo' -- $fili"; if ($?) {

print STDERR "Conversion of \"$fili\" failed with exit status $?.\n";

exit $?;

}

}

TIPS: The ps2png script needs the pnmcrop and pnmtopng commands, which can be resolved by

installing the netpbm packages:

$ yum install netpbm netpbm-progs # provide pnmcrop & pnmtopng etc.

17

Sum-over-states Approach

Similar to the above calculations, first we copy the following files from upper directory:





../evc/evc.cart.dat

to a work directory, say, sumstat.



shown as follows:

Then, perform the calculation by running the script file:

$ ./run

[sumstat]$ cat momap.inp

do_spec_sums = 1 # if use sum-over-states approach, 1 or 0

&spec_sums

DSFile = "evc.cart.dat" # input evc file

Ead = 0.075092 au # adiabatic excitation energy

dipole_abs = 0.92694 debye # Electronic Transition Dipole Absorption

dipole_emi = 0.64751 debye # Electronic Transition Dipole Emission

maxvib = 10 # maximum vibration quantum number

if_cal_ic = .t. # if do internal conversion analysis, .t. or .f.

promode = 24 # promotion mode (internal conversion)

FC_eps_abs = 0.1 # eps of Franck-Condon factor (absorption)

FC_eps_emi = 0.1 # eps of Franck-Condon factor (emission)

FC_eps_ic = 0.1 # eps of Franck-Condon factor (internal conversion)

FreqScale = 1.0 # frequency scaling factor

FreqEPS = 0.01 # eps of frequency

Seps = 0.00001 # eps of Huang-Rhys coupling constant eps = 0.00 #

debug = .false. #

FWHM = 500 cm-1 # broadening factor, full width at half maximum blocksize = 1000 #

testpoints = 1000 #

TEST = .f. #

flog = "spec.sums.log" # output log file reduce_eps = 0.001 #

/

#!/bin/sh


18

Finally, the result files are shown as follows:

Filename Meaning

spec.sums.abs.dirac.dat Absorption spectrum and vibrational transition quantum numbers

spec.sums.emi.dirac.dat Emission spectrum and vibrational transition quantum numbers

spec.sums.ic.dirac.dat Internal conversion and vibrational transition quantum numbers

with the set promode as promotion mode

spec.sums.log Logging file for sums-over-states aproach

spec.sums.spec.dat Absorption and emission spectrum

Plot the data from file spec.sums.spec.dat by using columns 4, 7, and 13, in Linux, we can use

Gnuplot to do the plotting, the plot script is shown as follows:

Then use the following commands to generate the graph:

$ gnuplot *.gnu

$ ps2png *.eps

$ display *.png

[sumstat]$ ls

azulene-s0.fchk momap.inp spec.sums.abs.dirac.dat spec.sums.emi.short.dat

azulene-s0.log nodefile spec.sums.abs.long.dat spec.sums.ic.dat

azulene-s1.fchk README spec.sums.abs.short.dat spec.sums.ic.dirac.dat

azulene-s1.log ref spec.sums.emi.dat spec.sums.log

evc.cart.dat run spec.sums.emi.dirac.dat spec.sums.spec.dat

log spec.sums.abs.dat spec.sums.emi.long.dat

[sumstat]$ cat spec.sums.spec.gnu

reset

set nogrid

set lmargin 10

set pointsize 1.0



set xlabel "Wave number, cm^{-1}" offset 0,0

set ylabel "Intensity, a.u." offset 0,0

set xtics nomirror

set ytics nomirror

set yrange [0:1.15]

set output "spec.sums.spec.eps"

plot \

"spec.sums.spec.dat" u 4:7 t "Absorption" w l lw 3 lt 1, \

"" u 4:13 t "Emission" w l lw 3 lt 2

19

Fig. 6 Absorption and emission spectrum by using sum-over-states approach

20

Verify Convergence of Correlation Function

Correlation function must be converged before obtaining any calculation results. To verify, plot a graph

using the first 2 columns in spec.tvcf.ft.dat, which are time and real part of the correlation function

(TVCF_RE). TVCF_RE should be very close to zero and stop oscillating before it reaches the integration time

limit. Figure 7 shows the distribution of a converged correlation function.

The Gnuplot plot script for the figure is shown as follows:

Then use the following commands to generate the graph:

$ gnuplot *.gnu

$ ps2png *.eps

$ display *.png


[sumstat]$ cat spec.tvcf.ft.gnu

reset

set nogrid

set lmargin 10

set pointsize 1.0



set xlabel "Time, fs" offset 0,0

set ylabel "TVCF (RE)" offset 0,0

set xtics nomirror

set ytics nomirror

set xrange [-80:80]

set output "spec.tvcf.ft.eps"

plot "spec.tvcf.ft.dat" u 1:2 t "" w l lw 3 lt 1

Date post:	06-Feb-2021
Category:	Documents
Upload:	others
View:	6 times
Download:	0 times

Tutorial 01 - shuaigroup · 2020. 1. 16. · MOMAP Tutorial - Fluorescence Spectrum Calculation...

Documents